biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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Installation issue where is the executable now? #434

Closed moldach closed 4 years ago

moldach commented 4 years ago

I believe I'm very close to having sambamba installed.

git clone --recursive https://github.com/biod/sambamba.git
cd sambamba
make

I should not that make ran successfully after downloading and setting a path to ldc:

(ldc-1.20.1)[moldach@cedar5 sambamba-0.7.1]$ echo $PATH
/home/moldach/dlang/ldc-1.20.1/bin

But now when I type sambamba into the console it say's the command can not be found. In older issues the exectuable was place in /build but I don't see that:

(ldc-1.20.1)[moldach@cedar5 sambamba-0.7.1]$ tree
.
├── BioD
├── contrib
│   └── shunit2-2.0.3
│       ├── CHANGES-2.0.txt
│       ├── contributors.txt
│       ├── LGPL-2.1
│       ├── README.txt
│       └── shunit2
├── cram
│   ├── exception.d
│   ├── htslib.d
│   ├── reader.d
│   ├── reference.d
│   ├── slicereader.d
│   ├── wrappers.d
│   └── writer.d
├── deb
│   ├── DEBIAN_CHANGELOG
│   └── makepackage.rb
├── doc
│   └── design.org
├── dub.json
├── etc
│   └── bash_completion.d
│       └── sambamba
├── gen_ldc_version_info.py
├── htslib
├── INSTALL.md
├── LICENSE
├── lz4
├── Makefile
├── Makefile.docker
├── Makefile.guix
├── Makefile.old
├── man
│   ├── README.md
│   ├── sambamba.1
│   ├── sambamba.1.ronn
│   ├── sambamba-flagstat.1
│   ├── sambamba-flagstat.1.ronn
│   ├── sambamba-index.1
│   ├── sambamba-index.1.ronn
│   ├── sambamba-markdup.1
│   ├── sambamba-markdup.1.ronn
│   ├── sambamba-merge.1
│   ├── sambamba-merge.1.ronn
│   ├── sambamba-pileup.1
│   ├── sambamba-pileup.1.ronn
│   ├── sambamba-slice.1
│   ├── sambamba-slice.1.ronn
│   ├── sambamba-sort.1
│   ├── sambamba-sort.1.ronn
│   ├── sambamba-view.1
│   └── sambamba-view.1.ronn
├── README.md
├── RELEASE-NOTES.md
├── run_tests.sh
├── sambamba
│   ├── depth.d
│   ├── fixbins.d
│   ├── flagstat.d
│   ├── index.d
│   ├── main.d
│   ├── markdup2.d
│   ├── markdup.d
│   ├── merge.d
│   ├── pileup.d
│   ├── slice.d
│   ├── sort.d
│   ├── subsample.d
│   ├── utils
│   │   ├── common
│   │   │   ├── bed.d
│   │   │   ├── file.d
│   │   │   ├── filtering.d
│   │   │   ├── intervaltree.d
│   │   │   ├── ldc_gc_workaround.d
│   │   │   ├── overwrite.d
│   │   │   ├── pratt_parser.d
│   │   │   ├── progressbar.d
│   │   │   ├── queryparser.d
│   │   │   ├── readstorage.d
│   │   │   └── tmpdir.d
│   │   └── view
│   │       ├── alignmentrangeprocessor.d
│   │       └── headerserializer.d
│   ├── validate.d
│   └── view.d
├── sambamba-ldmd-debug.rsp
├── sambamba-ldmd-release.rsp
├── scripts
│   ├── bioconda_push.sh
│   ├── bioconda_yaml_gen.py
│   ├── drone.yml.template
│   ├── dropbox.sh
│   └── randomize_bases.d
├── test
│   ├── benchmark
│   │   └── stats.org
│   ├── chr2_chr3_test_region.bed
│   ├── ex1_header.sam
│   ├── issue_193.bam
│   ├── issue_193.bam.bai
│   ├── issue_193_expected_output.txt
│   ├── issue_204.bam
│   ├── issue_204.bam.bai
│   ├── issue_204_expected_output.txt
│   ├── issue225.bam
│   ├── issue225.bam.bai
│   ├── issue225.out
│   ├── issue225.z.out
│   ├── issue_356.sam
│   ├── match_mates.bam
│   ├── mate_overlaps_1_3M_4M.bam
│   ├── mate_overlaps_1_3M_4M.bam.bai
│   ├── mate_overlaps_1_3M_4M.bed
│   ├── regression
│   │   └── issue_331_header.json
│   ├── test_depth.py
│   └── test_suite.sh
├── thirdparty
│   ├── mergesort.d
│   └── unstablesort.d
├── utils
│   ├── lz4.d
│   ├── strip_bcf_header.d
│   └── version_.d
└── VERSION

21 directories, 107 files
pjotrp commented 4 years ago

Check the other build systems. Travis is one.